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De novo transcriptome assembly: A comprehensive cross-species comparison of short-read RNA-Seq assemblers

Gigascience, 2019-05, Vol.8 (5)

2019

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Covasim: An agent-based model of COVID-19 dynamics and interventions

PLoS computational biology, 2021-07, Vol.17 (7), p.e1009149

2021

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Gib mir den Virus und ich sag dir den Wirt

Biospektrum, 2022-03, Vol.28 (2), p.225-226

2022

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Proteinortho: detection of (co-)orthologs in large-scale analysis

BMC bioinformatics, 2011-04, Vol.12 (1), p.124-124, Article 124

2011

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Rfam 14: expanded coverage of metagenomic, viral and microRNA families

Nucleic acids research, 2021-01, Vol.49 (D1), p.D192-D200

2021

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SAveRUNNER: A network-based algorithm for drug repurposing and its application to COVID-19

PLoS computational biology, 2021-02, Vol.17 (2), p.e1008686

2021

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EpiDope: a deep neural network for linear B-cell epitope prediction

Bioinformatics, 2021-05, Vol.37 (4), p.448-455

2021

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Prediction of conserved long-range RNA-RNA interactions in full viral genomes

Bioinformatics (Oxford, England), 2016-10, Vol.32 (19), p.2928-2935

2016

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Vitamin supplementation by gut symbionts ensures metabolic homeostasis in an insect host

Proceedings of the Royal Society. B, Biological sciences, 2014-12, Vol.281 (1796), p.20141838-20141838

2014

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Inclusion of Oxford Nanopore long reads improves all microbial and viral metagenome‐assembled genomes from a complex aquifer system

Environmental microbiology, 2020-09, Vol.22 (9), p.4000-4013

2020

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MicrobeTrace: Retooling molecular epidemiology for rapid public health response

PLoS computational biology, 2021-09, Vol.17 (9), p.e1009300-e1009300

2021

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Structural and functional conservation of cis-acting RNA elements in coronavirus 5'-terminal genome regions

Virology (New York, N.Y.), 2018-04, Vol.517, p.44-55

2018

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SynToxProfiler: An interactive analysis of drug combination synergy, toxicity and efficacy

PLoS computational biology, 2020-02, Vol.16 (2), p.e1007604-e1007604

2020

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pyTFM: A tool for traction force and monolayer stress microscopy

PLoS computational biology, 2021-06, Vol.17 (6), p.e1008364-e1008364

2021

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MGDrivE 2: A simulation framework for gene drive systems incorporating seasonality and epidemiological dynamics

PLoS computational biology, 2021-05, Vol.17 (5), p.e1009030

2021

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Software Dedicated to Virus Sequence Analysis "Bioinformatics Goes Viral"

Advances in virus research, 2017, Vol.99, p.233-257

2017

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FastTrack: An open-source software for tracking varying numbers of deformable objects

PLoS computational biology, 2021-02, Vol.17 (2), p.e1008697-e1008697

2021

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A fast machine-learning-guided primer design pipeline for selective whole genome amplification

PLoS computational biology, 2023-04, Vol.19 (4), p.e1010137-e1010137

2023

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MitoScape: A big-data, machine-learning platform for obtaining mitochondrial DNA from next-generation sequencing data

PLoS computational biology, 2021-11, Vol.17 (11), p.e1009594-e1009594

2021

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Genomic analysis of 61 Chlamydia psittaci strains reveals extensive divergence associated with host preference

BMC genomics, 2023-05, Vol.24 (1), p.288-17, Article 288

2023

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POMAShiny: A user-friendly web-based workflow for metabolomics and proteomics data analysis

PLoS computational biology, 2021-07, Vol.17 (7), p.e1009148-e1009148

2021

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RNA structure analysis of alphacoronavirus terminal genome regions

Virus research, 2014-12, Vol.194, p.76-89

2014

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SILGGM: An extensive R package for efficient statistical inference in large-scale gene networks

PLoS computational biology, 2018-08, Vol.14 (8), p.e1006369-e1006369

2018

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Structure learning for gene regulatory networks

PLoS computational biology, 2023-05, Vol.19 (5), p.e1011118-e1011118

2023

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Conserved RNA secondary structures and long-range interactions in hepatitis C viruses

RNA (Cambridge), 2015-07, Vol.21 (7), p.1219-1232

2015

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De novo transcriptome assembly: A comprehensive cross-species comparison of short-read RNA-Seq assemblers

Covasim: An agent-based model of COVID-19 dynamics and interventions

Gib mir den Virus und ich sag dir den Wirt

Proteinortho: detection of (co-)orthologs in large-scale analysis

Rfam 14: expanded coverage of metagenomic, viral and microRNA families

SAveRUNNER: A network-based algorithm for drug repurposing and its application to COVID-19

EpiDope: a deep neural network for linear B-cell epitope prediction

Prediction of conserved long-range RNA-RNA interactions in full viral genomes

Vitamin supplementation by gut symbionts ensures metabolic homeostasis in an insect host

Inclusion of Oxford Nanopore long reads improves all microbial and viral metagenome‐assembled genomes from a complex aquifer system

MicrobeTrace: Retooling molecular epidemiology for rapid public health response

Structural and functional conservation of cis-acting RNA elements in coronavirus 5'-terminal genome regions

SynToxProfiler: An interactive analysis of drug combination synergy, toxicity and efficacy

pyTFM: A tool for traction force and monolayer stress microscopy

MGDrivE 2: A simulation framework for gene drive systems incorporating seasonality and epidemiological dynamics

Software Dedicated to Virus Sequence Analysis "Bioinformatics Goes Viral"

FastTrack: An open-source software for tracking varying numbers of deformable objects

A fast machine-learning-guided primer design pipeline for selective whole genome amplification

MitoScape: A big-data, machine-learning platform for obtaining mitochondrial DNA from next-generation sequencing data

Genomic analysis of 61 Chlamydia psittaci strains reveals extensive divergence associated with host preference

POMAShiny: A user-friendly web-based workflow for metabolomics and proteomics data analysis

RNA structure analysis of alphacoronavirus terminal genome regions

SILGGM: An extensive R package for efficient statistical inference in large-scale gene networks

Structure learning for gene regulatory networks

Conserved RNA secondary structures and long-range interactions in hepatitis C viruses

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